Targeted genetic engineering of cells and organisms holds great promise for research and therapy. While some tools for site-specific modifications of genomic sequences have been developed, such as, for example, site-specific nucleases or nickases that can introduce double-stranded or single-stranded cuts in a genomic target sequence, the targeted integration, deletion, or inversion of sequences within a genome relies on relatively ineffective technologies, such as homologous recombination and gene targeting. Methods and molecular tools for direct manipulation of a target sequence within a genome are therefore highly desirable.